James Shapiro gets evolution wrong again

When is PuffHo going to realize that they’re publishing criticisms of evolutionary biology that are deeply misguided? Do they have no worries about misleading the public with bad science?

I refer to the recurring posts of my Chicago colleague James Shapiro, who is making a PuffHo blogging career out of attacking “neoDarwinism,” the modern theory of evolution. Not that we haven’t a lot to learn yet about evolution, but Shapiro has repeatedly been going after the importance of natural selection (see screenshot below) without offering a viable alternative. That is, Shapiro sees organisms as “self organizing” units controlled by “natural genetic engineering”, which of course doesn’t explain in the slightest why those organisms are adapted to their environments.

I almost don’t have the heart to criticize his latest piece, “Why the ‘gene’ concept holds back evolutionary thinking“, except that there may be some people out there (including the science editor of PuffHo) who think that Shapiro’s lucubrations are scientifically supported. They aren’t: they’re the misguided ideas of a contrarian who thinks that he alone has the key to overturning the modern theory of evolution.

Now we do know a lot more about the genome than we did when Beadle and Tatum proposed their “one gene/one enzyme hypothesis.” We know now that there are more than just protein-producing units in the DNA: there are parts of those units that regulate their expression (though this was posited by Jacob and Monod in the early Sixties), there are non-coding regions within genes (“introns’) that get snipped out, there are “transcription factors” (protein-producing genes) that regulate the expression of many other genes (e.g., Hox genes), and now we know that there are “microRNAs”, small molecules that serve to shut off genes.

In other words, we’re starting to learn how genes (originally defined as “stretches of DNA that make proteins”) are regulated, and the definition of a “gene” has become somewhat blurry. But I still don’t see the harm in using its original definition so long as we realize that the genome comprises much more than just protein-coding units. (The ENCODE project, however, has drastically oversold the notion that what we thought of as “useless” DNA is really functional. There’s still a lot of junk in our genome that doesn’t seem to do anything.)

Anyway, Shapiro’s point is that our modern understanding of how genomes are constructed and regulated when building organisms has completely overturned the modern theory of evolution—including the importance of natural selection—by making the notion of a “gene” fuzzier.

He’s wrong, and he’s wrong because he doesn’t seem to understand how evolution works.

Shapiro notes:

The basic issue is that molecular genetics has made it impossible to provide a consistent, or even useful, definition of the term “gene.” In March 2009, I attended a workshop at the Santa Fe Institute entitled “Complexity of the Gene Concept.” Although we had a lot of smart people around the table, we failed as a group to agree on a clear meaning for the term.

The modern concept of the genome has no basic units. It has literally become “systems all the way down.” There are piecemeal coding sequences, expression signals, splicing signals, regulatory signals, epigenetic formatting signals, and many other “DNA elements” (to use the neutral ENCODE terminology) that participate in the multiple functions involved in genome expression, replication, transmission, repair and evolution.

. . .A particularly important novelty highlighted by the Genome Biology paper is the unexpected and burgeoning role of so-called “non-coding” RNAs (ncRNAs) in all aspects of genome function. Cells transcribe many functional ncRNAs from so-called “intergenic” regions that had no functional importance according to the genocentric theory.

From an EVO-DEVO point of view, it is important to note that many morphogenetic changes in evolution occur at regulatory sites rather than coding sequences. Moreover, we continue to discover how many of these changes occur “intergenically” and involve supposedly “selfish” mobile elements. . .

. . . Conventional thinkers may claim that molecular data only add details to a well-established evolutionary paradigm. But the diehard defenders of orthodoxy in evolutionary biology are grievously mistaken in their stubbornness. DNA and molecular genetics have brought us to a fundamentally new conceptual understanding of genomes, how they are organized and how they function.

I’m baffled. Yes, these new discoveries are exciting, but they have absolutely no bearing on two issues: 1) whether natural selection acts on these new bits of the genome, and 2) whether natural selection is the primary process that produces “adaptations” in organisms. After all, all these units of the genome are still bits of DNA residing within the genome (usually on chromosomes), and therefore must obey the laws of population genetics. And those laws say that if a bit of DNA helps the organisms’s reproduction, it proliferates. If it hurts the organisms’s reproduction, it gets expunged from the population. That’s natural selection. Ergo, all of those genomic things that regulate other genes are subject to natural selection (and, of course, genetic drift).

In fact, there’s little doubt (except in the mind of contrarians like Shapiro) that the mechanisms of gene regulation themselves evolved by natural selection.

Shapiro still hasn’t provided a credible alternative theory of how adaptive features of an organism arise. “Natural genetic engineering” certainly can’t. And until he provides a credible theory, he will be a voice crying out in the wilderness, thinking himself a paradigm-changer but sounding more like a crank. For it is sentences like these—the last in Shapiro’s piece—that verge on the crankish:

Shortly before he passed away, Kurt Vonnegut told a radio interviewer that the public senses something amiss with what they have been told about evolution. Maybe the new, high-tech understanding of genomes will help reverse the disastrously low level in the U.S. of public understanding of evolutionary biology.

That is real hubris—to think that if evolutionists would only agree with your bogus biological notions, creationism would decline! Nope, it’s not misunderstanding of modern genetics that buttresses creationism—it’s religion. Only someone completely blinkered could think otherwise.

It isn’t the “gene concept” that holds back evolutionary thinking; it’s not only creationist opposition, but also people like Shapiro who, without any scientific support, mislead readers by arguing that the modern theory of evolution is fatally flawed.

Finally, from the comments, here’s Shapiro’s explanation about why I criticize him:

Sorry, Dr. Shaprio, but I’ve built my career on understanding the genetic basis of how species arise, not on “accepting the central role of natural selection as a creative force in evolution.” I do think natural selection is the only viable explanation for the adaptations of organisms, and we have plenty of evidence for that contention, but it’s hardly the cornerstone of my career.

And, thank Ceiling Cat, I haven’t aspired in my middle age to overturn well-established paradigms. The reason I defend natural selection is not because I’m somehow wedded to that idea to buttress my career, but because it is still the best explanation that we have for adaptations.

75 Comments

I read through the piece before reading Jerry’s comments and “I’m baffled” pretty much summed it up for me. I didn’t see anything in it that suggested that we should be tossing Natural Selection. If anything, what I read (in a nutshell) was that we’re gaining new knowledge about how genomes work and we may have to rethink what happens at the molecular level. Then there’s a punchline about “…the diehard defenders of orthodoxy in evolutionary biology are grievously mistaken in their stubbornness…” I don’t get it. The piece is irresponsible in my opinion.

Lastly, his response to the commenter is a classic conspiracy-theory, crank response. He doesn’t actually respond to his critics arguments, he just rights them off as being entrenched in a kind of scientific dogma for career reasons and then offers up a link to another one of his articles. Amateurish in my opinion…

Wendell, I explained why that is bad science; it says natural selection is a minor force, of little importance in evolution, but gives no evidence for that, bur rather throws sand in our eyes by listing a bunch of genetic mechanisms (all of them subject to natural selection).

Lay off the snark, for that is what this is. If you have a valid counterargument, explaining why Shapiro is right, make it.

Hmmm, people announcing the revolution that is coming. Just make the revolution instead of announcing it so much. It’s not like biology doesn’t accept very important discoveries that have a big, lasting impact.

Concerning stuff related to evolution and genetics, for example you have Ohno, Kimura and Lewontin greatly changing our view of what genes and genomes look like and what’s going on most of the time at the molecular level. So there. Important contributions to science. Make one, why don’t you?

You’ve found me out. I admit it, I was referring to a book. How could I have been so foolish! But you have helped me see the light. I’ve taken all my books and burned them. Neither wisdom nor truth can be found in a book. Certainly no sound science.

This notion of scientists building their careers on accepting dogmas (if only it were that simple…) as well as the existence of supposed scientific conspiracies that guard certain taboos is also a favorite argument of creationists. In reality, fame and fortune :-) await the scientist who can overturn an accepted theory or paradigm. Of course, as Richard Dawkins noted, extraordinary claims require extraordinary evidence, and neither the creationists nor Dr. Shapiro provide any evidence against the role of natural selection, to say nothing of anything extraordinary.

Carl Sagan popularized this as “Extraordinary claims require extraordinary evidence”.[15] However, this may have been based on a quote by Laplace which goes, “The weight of evidence for an extraordinary claim must be proportioned to its strangeness.”[citation needed] This, in turn, may have been based on the statement “A wise man, therefore, proportions his belief to the evidence” byDavid Hume.[16]

Is there even a substantive difference between “natural genetic engineering” and natural selection? Suppose nature is in fact a genetic engineer. How might it implement these engineering feats? One pretty obvious is way is by throwing out things that don’t work and reusing things that do. Where “things that work” are traits that allow an organism to produce more offspring.

I took “natural genetic engineering” to be a reference to various sorts of hand-waving speculation about quantum computers hidden in the junk DNA that purposely modify genes in non-random ways to meet adaptive needs.

Of course there’s no evidence whatsoever that any such thing exists or is even possible. But that doesn’t stop people from proclaiming it as the next great paradigm shift in evolutionary thought.

Ougaseon, thre is an enormous difference between NGE and NS. I am on the last chapter of Shapiro’s book now. He doesn’t seem to give much credit to selection, nor should he. Selection really can’t do anything constructive, as he correcrtly points out early in the book.

I am not yet entirely clear on what he means by NGE, and I must finish the book to find out. So far, I find the book to be very detailed and loaded with pertinent citations, and I have found nothing to disagree with so far. Excellent book.

IntelligentAnimation, selection demonstrably CAN do something constructive and anyone saying otherwise is confusing evolution with individual change, i.e. confusing individual traits with population/species traits. (This confusion might be the source of misunderstanding for many people.) Evolution is a population-level phenomenon: individuals mutate but they do not evolve.

It is true that new variants have to arise in an individual, independent of selection. However, we do not say that trait has “evolved” until it reaches a high frequency or even reached (effective) fixation. For example, certain point mutations cause polydactyly (extra fingers and toes) in humans but we do not say that humans have “evolved six fingers”. Selection is the process that drives a variant through (or from) a population, thus contributing to its evolution. I hope that makes sense.

For humans, a mutation usually has to reach a frequency of 1% before being considered a polymorphism. This is somewhat arbitrary but it needs to be in at least two individuals and generations: otherwise, lethal or sterilising mutations would constitute a polymorphism and this would make the concept pretty useless. (As would saying that something had “evolved sterility” because a single individual had a sterilising mutation.)

The only way to non-randomly go from 000001000 to 111111111 is selection. So yes, NS can be constructive and produce an *evolved* trait.

Cabbages of Doom, if the supposed constructive powers of selection are demonstrable, then it would make sense to demonstrate them. The numeric example you gave does not offer up anything helpful. Perhaps you could explain it?

If extra fingers did become fixed in the population (yes, I find your 1% number to be arbitrary and useless) then it would make no sense to say selection “constructed” it.

Selection didn’t “produce” anything, nor can it. To “not destroy” is different than saying “construct” or “produce”.

Selection is just a word used to describe the success (or lack thereof) of a phenotypical trait. Selection is not an actual thing that actually does anything.

IntelligentAnimation, I am not sure if this is a game of semantics or a genuine question. Selection is not simply just a word to describe success of a phenotypic trait, though – there has to be causal linkage with a heritable variant for it to be “selection” in the sense of “Natural Selection”. Differential success by itself is not enough (that’s essentially random genetic drift).

The “constructive” element – or the answer to your question elsewhere regarding what it “explains” – is that directional fixation of heritable traits that can, over time, become quite complex and fine-tuned adaptations.

(Not all selection is “positive” or adaptive, of course and, yes, mutations are also needed. I am not sure who would deny this nor why it somehow means that selection is not important. BOTH mutation and selection are important for adaptive evolution!)

The good professor could also point out that that a huge body of evidence supports natural selection. On the other hand the deniers have to rely on the unsubstantiated claims of a handfull of fringe contrarians.

That’s like saying E=mc^2 doesn’t mention gravity, so relativity doesn’t explain the orbits of the planets. There is a difference between the fundamental mechanism of a theory and its explanatory power. For relativity and evolution by natural selection both, the mechanisms are straightforward yet have massive implications that allow us to make sense of the world around us.

It always makes me lauggh when Science deniers try to disprove evolution via biology. For sure they can and should question any gaps in our knowledge in this area but i for one will always refer them back to providing an alternative explanation for the fossil sequence and the fact that over geological time species change with time where sponges & worms appear before first fish, fish appear before first tetrapods and so on for amphibians, reptiles, mammals & birds.
Until they can address this most fundamental of issues, then they are wasting their time attempting to sound clever by misrepresenting the hard work of others.

I’m often trying to disabuse people of excessively simplistic mental categories. Biblical sexuality laws lose their credibility after you realise that not all individuals are born with one unambiguous sex. Nationalism is exposed when you start to explore edge cases. To explain evolution to a creationist one has to emphasise where the blurred nature of populations is incompatible with their platonic ideal of species (even if this may offend traditional biologists i.e. taxonomists).

I haven’t read Shapiro’s previous articles, but in this one he basically just seems to be saying that the preconceived ideal of “genes” (as complicated monolithic units) is over-emphasised, to the detriment of teaching genetic evolution with all its nuance. That there’s a rich landscape between protein-coding and total-functionlessness. That neglecting this intervening space tends to be associated with an overly adaptionist view of evolution which discounts the large role played by neutral evolution. I can’t seem to put my finger on what has deserved the vitriol here?

riment of teaching genetic evolution with all its nuance. That there’s a rich landscape between protein-coding and total-functionlessness. That neglecting this intervening space tends to be associated with an overly adaptionist view of evolution which discounts the large role played by neutral evolution.

there lies the rub: this connection is non-existent. Shapiro made it up.

Shapiro is not pushing for “neutral evolution” (by that, I take it you are thinking of drift?), because he doesn’t even understand what the term means.

Taken as it stands I have no quarrel with your comment. I am puzzled however regarding what relevance it has to Dr. Shapiro. If your comment was meant to apply to him, then it is the height of stupidity.

“Natural genetic engineering”? From time to time I see some commenter on other websites who (e.g. Pigliucci’s) insists that even bacteria evolve strategically and in a self-guided, intelligent way.

Two questions: What organ do these cranks think that individual cells or bacteria can be intelligent with? And, from a scientific point of view, what would falsify their idea, i.e. how do they think a world would look like in which there was not what they call natural genetic engineering?

As a molecular biologist I have no idea what he is going on about. Creating controversy where there isn’t any (once again).

Yes, there are introns, exons, micro RNAs, long non-coding RNAs, short non-coding RNAs, promoters, enhancers, insulators, alternative splicing, epigenetic silencing, copy number variation, single nucleotide polymorphisms etc… etc… And natural selection can act on any of these. People may argue over semantics like “what defines a gene” but so what?

Congratulations Shapiro you read a molecular biology textbook. Then you made up the “diehard defenders of orthodoxy in evolutionary biology are grievously mistaken in their stubbornness” so you had something to write about.

There are so many interesting scientific discoveries you could be writing about. Maybe even try to educate your readers a bit. Instead you choose to misrepresent science in the media once again – shame on you!

I have no problem with snark. In fact is an excellent format for conveying a great deal of information in a few words. Let’s examine what the posted ‘snark’ is actually saying:
1) Shapiro has a smattering of information on molecular biology.
2) He does not realize just how limited his information on the subject actually is.
3) Because of the disconnect between what he thinks he knows, and what he actually knows, he has made a fool of himself by his grandiose pronouncements on the subject.
4) You however, being much better informed on the subject, can easily point out the absurdities of what he has said.

I suggest that there is a vast gulf between the ‘implications’ of the posted snark and reality.

Okay, Mr. Deep Understanding, let’s probe your knowledge of evolution. Maybe you can improve mine. Can you explain how and/or why natural selection does not operate on the listed genetic elements, even though they are presumably producing phenotypic/adaptive benefits? This is Shapiro’s ‘new view’, that genetic material self-engineers its way to these changes while somehow bypassing selection. I find this mystifying. If genetic material self-engineers ‘toward’ organismal benefits, while bypassing selection, how is it that most species that have ever lived are now extinct, courtesy of natural selection?

I am genuinely interested to know, because these things prevent me from accepting the validity of his new theory of evolution – a view which I have no reflexive hostility toward.

in fact, just like Behe, just because someone has a degree in molecular or cellular biology doesn’t preclude them from saying really, REALLY, inane stuff about any field of endeavor.

sometimes even their own.

Michael Egnor is a neurosurgeon at Stony Brook, the same place Douglas Futuyma is from, but says the most inane and ridiculous crap about evolutionary biology one can imagine.

Behe, Shapiro, Wells… all of these people have advanced biology degrees, and STILL say the dumbest crap. Behe at least was forced to retract some of the dumb stuff he has said when on the stand at Dover. The others are afraid to try to support their contentions in a court of law, because they KNOW they would be laughed out of court in minutes.

the reason people like Wendell here lap them up is simply because people like Wendell are authoritarians, who only will listen to people who tell them the “right” things.

Wendell doesn’t understand science, he’s just a sheep that pretends he does.

Can you provide the source for the statement that genes were: originally defined as “stretches of DNA that make proteins”?

I thought that “gene” was originally defined by Wilhelm Johannsen as a structural/functional unit of heredity, which makes Shapiro even less right. There is no problem with non-coding DNA being “genes” in the sense of functional units of heredity (and contributing to Natural Selection).

I totally agree that there is not (and cannot be a) single, clear, all-encompassing definition of a gene in terms of DNA – there is a continuum of linked genetic information – but I fail to see how this presents any problem for Natural Selection or genetic evolutionary theory. It’s just another example of the kind of confusion you get when you try to digitise a continuum. Surely someone who knows as much about recombination as Shapiro should know this?

So I don’t know Shapiro. Isn’t he just one of those that needs to pry a nonexistent gap open for his more or less open creationism? The key term seems to be “natural genetic engineering”, where you can equivocate on the meaning of “natural”.

Or is he set on making a name by “overturning the modern theory of evolution”?

And I guess one doesn’t exclude the other, if you are really deluded/optimistic.

Professor Shapiro is not a creationist, but his emphasis on being contrarian sometimes makes it hard to see that.

He actually did some quite good research at one time showing colonies of microorganisms had abilities at things like chemical communication and resultant coordinated action that eventually came to be accepted against the former prevailing wisdom that microbes were far too primitive to be capable of such things.

The problem is that Shapiro then took this as his template for future conduct, whether merited by experimental results or not. Fairly recently (1990s – 2000s), he became an enthusiast of “directed evolution,” which posited that microbes were self-directing advantageous mutations. However, the initial optimism of this movement faded as researchers came to learn that while microbes under certain kinds of stress would mutate *faster*, there was no indication they could mutate *better*. (See, e.g., Lenski’s experiments showing microbes requiring tens of thousands of generations for just a handful of mutations leading to a tremendous reproductive advantage.) Even those who had published the early “directed evolution” research papers with Shapiro fell by the wayside. Only Shapiro has remained convinced that, as in earlier days, his views of the capabilities of microbes will eventually be proved right. In his view they are all little genetic engineers, causing non-random mutations in themselves in order to adapt optimally to their environments.

The reference to Kurt Vonnegut in his penultimate paragraph — presented without link, citation, or even a general description of the circumstances of the purported interview — is an especially cheap shot by Shapiro, a back-handed appeal to authority offered apparently to obfuscate, rather than make any point.

As best I can tell, the reference is to some inchoate comments Vonnegut made during an interview with NPR in 2006. Vonnegut’s point there concerned “tribalism” in American society, not the science of biological evolution. (In any event, during interviews Vonnegut frequently parodied those whose positions he opposed by ostensibly espousing them in exaggerated fashion.)

When I bought my iPad I download Shapiro’s free eBook called Evolution: Views from the 21st Century. He seemed to suggest that cells were intelligent, among many other outrageous claims. Bring the crazy!

Wait — wasn’t he here posting comments in a thread a little while back?

I seem to remember thinking him a Creationist. At the least, he was coming down hard on a side not consistent with evolutionary biology. I don’t remember him offering any coherent alternative; rather, he just threw rocks at Darwin. Something utterly bizarre about how Darwinism can’t explain multiple drug resistance because some of the DNA comes from horizontal gene transfer.

He never got ’round to the “Ergo, Jesus,” but it sure felt like it was going to be his next response.

He has always been very coy about what, if any, religious beliefs he has. He commented on Sandwalk after a critique of his work and Larry Moran then asked him directly if he believed in god. He didn’t respond (which I think we can take as a ‘yes’).

He has apparently criticized at least some aspects of ID, if not ID outright, but also worked on a paper with Richard Sternberg of ‘Expelled’ fame. So he is seemingly presenting a ‘third way’ – some sort of teleological evolution.

Shapiro seems to ignore the fact that natural selection can be expected regardless of its role in the evolutionary theory. Forget evolution, even if we popped into existence 10 minutes ago, fully formed and functional, what does he think happens next, when the environment changes? Will organisms still thrive even though they will be no longer adapted to the new environment? The actual mechanisms of genetic variability aside, once we agree that this variability exists, and that genotype (regardless of how we define a single gene) determines phenotype, then we must agree that eliminating certain phenotypes from the population will change the genetic pool.

The idea that a gene is a stretch of DNA that codes for a single protein is actually rather new. Just look at the care Dawkins takes with defining it in The Selfish Gene. The meaning he settles on is not mere protein coding, and covers all the various complexities found in the DNA system.

Shapiro has a point, slightly. If you think of genes as local features of a sequence, you could miss out on the significance of chromosomal rearrangements, and of any cut-and-paste mutations larger than what you consider as a gene. Speciation need not involve the accumulation of individual genetic differences in spatially separated populations until they can no longer interbreed when they again come into contact. It can happen instead by chromosomal rearrangement that renders some combinations of individuals unable to reproduce.

The story he really wants to tell, however, starring himself in the role of Galileo, is pure bunkum.

There is something generally nasty about this fellow – he is a one man band, and his first loyalty isn’t to a creationism free world. He wants to nitpick and hasn’t the graciousness to see excellent work when it is done. There is an somewhat crude metaphor in Australia about either being in the tent pissing out or outside the tent pissing in. He wants to appear as if he is inside the tent and just pisses on fellow evolutionists. His arguments are so convoluted they can only confuse rather than clarify. There is some sort of intellectual dishonesty masquerading as complexity which then becomes confusion. This just casts doubt so that those who are against evolution can create a dust storm. The climate change people also work with doubt, as did the pro-smoking lobby.

In my opinion, Shapiro is not so much against natural selection as he is for non-random mutation.

That’s right. He thinks mutation is non-random, read ‘purposeful’, read ‘directed’. If mutation is non-random, this would make evolution teleological. That, I suspect, is his paradigm shift in thinking about evolution.

I also suspect that Shapiro has God as the director but, if so, he keeps that hypothesis well hidden.

More importantly, he never actually demonstrates that mutation is non-random. Conversely, all of his examples are easily explained as the result of random mutation and (non-random) natural selection

Why doesn’t Dr. Shapiro get his ideas published in a peer-reviewed publication like Evolution”? Surely that is the proper forum for their adjudication, f they’re so solid and paradigm shifting, and *not* the woo-filled PuffHo.

I’m no expert on this but I think that what Shapiro is saying is that only changes to the DNA can be explained by natural selection.

If all the other bits of stuff arise as a result of the DNA and then these somehow contribute to functionality changes, the root data (the DNA) remains unchanged and so no change to the DNA would be transmitted during reproduction.

If no DNA change occurs then any functionality changes would have to be as a result of interaction with a change in the environment. So in this case the data that had changed would be held within the environment not the chromosome.